Influenza A Virus in Swine Surveillance

Fiscal Year 2018 Quarterly Report

Surveillance Summary for First Quarter FY 2018: Oct. 1 – Dec. 31, 2017

Report Summary1

• This report covers the first quarter (Q1) of fiscal year (FY) 2018, from Oct. 1 – Dec. 31, 2017.

• Where relevant, the report also includes previous years’ data for historical perspective. 

• The report provides data from both national and regional levels.

• In FY 2018 Q1, 7,842 samples were submitted for influenza A virus in swine (IAV-S) surveillance 

from 2,644 accessions. 

• H1N1 was the predominant subtype.

• Over the past 8 quarters, H1N2 predominated in Regions 1, 2, 3, 4 and 5. When regions are 

recorded as “unknown,” H1N2 predominates as well (see map in regional section). 

• Limited accessions from a region can skew data and lead to misinterpretation. Therefore, less 

inference can be applied to results from Regions 3, 4, and 5.

• All IAV-S submissions are voluntary and based on clinical case submissions to veterinary 

diagnostic labs. These data are not a statistically representative sampling of the U.S. swine 

population.

• Due to the voluntary nature of this surveillance, the information in this report cannot be used to 

determine regional and/or national incidence, prevalence, or other epidemiological measures, 

but it may help identify IAV-S trends. 

Introduction

This report, based on data received as of March 2, 2018, provides a brief update on the status of 

national surveillance for IAV in swine for producers, swine practitioners, diagnosticians, and the public. 

Summaries in this report may differ from those provided in past reports due to the regular addition of 

data from participating laboratories. Reporting months are based on the month the sample was 

collected. The USDA-APHIS website provides general information about the IAV-S surveillance program 

at https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/animal-disease-information/swinedisease-information/ct_siv_surveillance

The IAV-S surveillance program is voluntary and, as a result, the accessions and samples submitted 

represent a subset of the swine population. Submitted samples should only be collected from animals 

 1 In November 2016, VS modernized the process that prepares and stages laboratory results data for reporting. Consequently, 

VS recognizes there is a small difference in previously reported summary numbers for IAV-S surveillance. The results in this 

report reflect updated and corrected numbers achieved with the modernized data process.

Animal and 

Plant Health 

Inspection 

Service

Veterinary 

Services

March 2018
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displaying influenza-like illness. Due to its voluntary nature, this surveillance system does not entirely 

represent the total U.S. domestic swine population. Therefore, the data cannot be used to determine 

IAV-S prevalence or other epidemiologic measures in the swine population. However, the data may help 

identify trends in influenza in swine. 

When the submitter does not report relevant information, data are recorded as “unknown.” Summaries 

in this report may differ from those provided in past reports due to the ongoing addition of data from 

participating labs. Reporting months are based on the month when the sample was collected. 

A laboratory accession is generally a set of samples collected at a single premises on a single day and 

received at the laboratory. While a nasal swab or lung tissue sample represents a single animal within 

the herd, a single oral fluid sample may represent one to two pens of animals in a herd. A positive 

sample status is based on the screening matrix real-time reverse transcriptase polymerase chain 

reaction (rRT-PCR). The subtype is based on the rRT-PCR- subtyping assays and sequencing if the sample 

is sequenced. Virus isolation (VI) and sequencing are only attempted on rRT-PCR positives meeting 

criteria listed in the testing algorithm posted on the web 

(https://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/appendix_c_testing_g

uidelines.pdf ). Phylogenetic analyses are based on successful sequencing results, with sequences 

deposited into GenBank®, the public sequence database.

Program Updates

Virus isolates from NVSL. Virus isolates acquired through USDA’s IAV-S surveillance are sent to the 

National Veterinary Services Laboratories (NVSL) in Ames, IA, and deposited into the IAV-S virus 

repository. Testing labs post the genomic sequences from the isolates into GenBank®, a publically 

accessible database maintained by the National Institutes for Health. USDA swine surveillance influenza 

A virus isolates can be identified in GenBank® by their eight-digit barcode designations in the virus 

name, e.g. A/swine/NY/A01104005/2011(H3N2). The information in GenBank® will usually list “USDA 

Swine Surveillance” or similar in the Consortium field. The majority of available isolates will have H and 

N sequenced, but some will also have full genome sequencing completed, including the M gene. The 

repository contains over 3,000 viruses. NVSL makes these viruses available to the public upon request.

Instructions for repository IAV-S isolate requests can be downloaded from here: 

https://www.aphis.usda.gov/animal_health/lab_info_services/downloads/OrderingIAVSRepositoryIsolates.pdf

The Influenza Research Database (IRD). https://www.fludb.org/brc/home.spg?decorator=influenza

The Influenza Research Database (IRD) is an integrative and comprehensive publicly available database 

and analysis resource to search, analyze, visualize, save, and share data for influenza virus research. It 

provides a bioinformatics resource to support scientific research on influenza virus. Important and 

reliable public sources of genomic, proteomic, annotation surveillance, experimental data has been 

identified, and data has been obtained and integrated into the IRD database. Following collaboration by 

Tavis Anderson and Amy Vincent at USDA’s Agricultural Research Service (ARS), the IRD has 

implemented the newly proposed Global Swine H1 Classification scheme. Major functions include: 

• Clade classification of all H1 sequences in IRD regardless of host.

• Sequence search based on H1 clade annotations.

• Clade assignment tool for user-provided H1 sequences.

• Phylogenetic tree decoration based on H1 clade annotations.

• Comparison of H1 sequences by M<eta-CATS using H1 clade material.
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The IRD website reports that the USDA Swine Influenza Surveillance Consortium submitted 956 influenza 

sequences to GenBank® during July-September 2017 using the IRD sequence submission tool. 

IAV-S Surveillance Objectives

USDA’s National Surveillance Plan for Swine Influenza Virus in Pigs (July 2010) describes the current 

surveillance system for IAV-S in detail. The surveillance objectives are to: 

1. Monitor genetic evolution of endemic IAV in swine to better understand endemic and 

emerging influenza virus ecology; 

2. Make influenza isolates from swine available for research and establish a data management 

system to facilitate genetic analysis of these isolates and related information; and 

3. Select proper isolates for the development of relevant diagnostic reagents, updated

diagnostic assays, and vaccine seed stock products. 

Objective 1. Monitoring genetic evolution of endemic IAV in swine to better 

understand endemic and emerging influenza virus ecology

Objective 1 is met through the submission of diagnostic laboratory samples to the surveillance system, 

collection of the viruses that are isolated from the samples, and analysis of the HA and NA sequences 

that are generated at the NAHLN laboratories and posted into GenBank®. Each month selected viruses

undergo whole genomic sequencing by NVSL. Phylogenic analysis of the genetic sequences is provided 

through an interagency agreement with the USDA-ARS National Animal Disease Center (NADC). 

National Surveillance Data Summary

From FY 2011 through FY 2016, the total number of accessions and samples submitted rose over time.

Changes initiated in FY 2016 have resulted in decreased laboratory accessions and samples, but have

resulted in a higher percentage of accessions that yield a virus that can be sequenced and analyzed. For

FY 2018’s first quarter, 7,842 samples were tested from 2,644 accessions (Figure 1) for a fiscal year-todate total of 7,842 samples and 2,644 accessions. Figure 2 shows the overall trends in total accessions, 

PCR-positive accessions, subtyped accessions, and VI positive accessions.
Figure 1. Number of IAV-S laboratory accessions and samples tested in swine, FY 2011 through FY 2018 Q1
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Figure 2. Accessions submitted, subtyped accessions, positive accessions, and VI positive accessions over time with trend lines, FY 2011 through FY 2018 Q1
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Figure 3 shows the number of subtype detections in FY 2018 Q1. The total number of samples subtyped was 367, including 140 H1N1, 111 H1N2, 

102 H3N2, 0 H3N1, and 14 mixed.

Figure 3. Number of subtype detections in FY 2018 Q1
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Figure 4 breaks down accessions by rRT-PCR subtype from FY 2011 to FY 2018 Q1. H1N1 remains the major subtype over the course of the 

surveillance; however, H1N2 and H3N2 detections have increased substantially since 2012 and H1N1 was the most predominant subtype in the 

first quarter of FY 2018. 

Figure 4. Number of subtypes, FY 2011 through FY 2018 Q1
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Figure 5 displays the number of VIs attempted, the number of those attempts that were positive, and the number of positive VIs that are 

submitted to GenBank. 

Figure 5. Number of virus isolations attempted, positive virus isolations, and GenBank submissions from FY 2014 through FY 2018 Q1

When accessions were evaluated by age-class for the first quarter, the following observations were noted. H1N2 was the most common subtype 

among suckling and nursery pigs. H1N1 was the most common subtype among grower/finishers. Sow/boar had limited testing, with only 11

samples of which were two were H1N1, four were H1N2, four were H3N2, and one was mixed. Among accessions for which the age class was 

unknown or not recorded, H1N1 was the predominant subtype (Table 1). Lung samples were the most successful at providing positive virus 

isolation and submission to GenBank (Table 2).

0

100

200

300

400

500

600 Number of virus isolations attempted

Number of virus isolation positive samples

Number of samples sequenced and sent to GenBank
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*Accessions may include samples with multiple specimen types. In these cases, individual accessions are counted in more than one specimen type category. 

**Other includes specimen types recorded as swab, mixed tissue, or unknown.
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Regional surveillance data

In this section, we present data in five different regions (Figure 6) to parse the analysis across regions. 

These regions are based on current USDA administrative districts for simplicity; these divisions do not 

represent specific industry distribution. Submissions are voluntary, as is any identifying information 

accompanying the submission (except the State of animal origin), and therefore no sampling strategies

can be applied to the regions. 

Figure 6. A map of the regions 

for national IAV-S surveillance

Summary of Regional Data from ARS

Table 3. Summary of predominant subtypes in each region for FY 2016 Q1 through FY 2018 Q1

Most Predominant HA/NA phylo-types overall:

H1N1 (Gamma H1/Classical N1) 

H1N2 (Delta1a H1/2002-N2) 

H3N2 (hu-like_2010 H3/2002-N2) 

Region 1 (Total HA/NA: 277)

Gamma H1/Classical N1

Delta2 H1/1998-N2

Alpha H1/2002-N2

Region 2 (Total HA/NA: 1,083)

Most diversity of all regions

Gamma H1/Classical N1

Delta1 H1a/2002-N2

Hu-like_2010 H3/2002-N2

Region 3 (Total HA/NA: 124)

Delta1a H1/2002-N2

Gamma H1/Classical N1

Hu-like_2010 H3/2002-N2

Region 4 (Total HA/NA: 138)

Delta1b H1/2002-N2

IV-A H3/2002-N2

Gamma H1/Classical N1

Region 5 (Total HA/NA: 7)

Low participation

Three Delta 1b H1/2002-N2

One each of:

Alpha H1/2002-N2

Hu-like_2010 H3/2002 N1

IV-A H3/2002-N2

Delta1a H1/1998-N2

Figure 7 shows the distribution of rRT-PCR subtyped accessions among the five regions for Q1 FY 2016

through Q1 FY 2018. Regions 1, 2, 3, 4, and 5 demonstrate H1N2 as the predominant subtype. For 

regions recorded as “unknown,” H1N2 was also the predominant subtype.

Region 1

Region 2

Region 3

Region 5

Region 5 Region 3

Region 4
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Figure 7. Percentage of subtyped accessions by region for FY 2016 Q1 through FY2018 Q1

Regional phylogenetic analysis

Phylogenetic analysis of sequences from the IAV-S surveillance system

Phylogenetic analysis of gene sequences of the influenza A virus in swine is conducted to further 

examine the genetic changes that occur in HA, NA, and M genes, when available, of this rapidly changing 

virus. Through collaboration with ARS, a dataset2 of 517 isolates with published sequences in GenBank®

was characterized by phylogenetic analysis in Q1 FY 2018. This analysis provides information on the 

genetic diversity and evolution patterns of influenza in swine and allows for inferences about population 

and/or vaccine immunity.

The following series of bar charts parse the data into an approximate 2-year window by quarters and 

subtypes for each region, followed by charts further parsing the H1 and H3 subtypes into phylogenetic 

clades. Regional charts depicting the various combinations of HA and NA are available in Appendix 1. 

 2 The ARS dataset is comprised of IAV-S surveillance isolate sequences that were posted in Genbank. This represents only a 

subset of the complete IAV-S surveillance dataset that includes PCR diagnostic test-based results as well as sequencing results. 

Therefore, ARS dataset results, such as subtype percentages, differ from the complete IAV-S dataset results provided in other 

sections of this report.
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Figure 8. Virus type by region 2-year summary Q2 FY 2016 to Q1 FY 2018

Figure 8 demonstrates the four subtypes H1N1, H1N2, H3N1, H3N2, and mixed subtypes across the five 

regions. Regions 1 and 2 reported the most submissions, with a mixture of mostly H1N1, H1N2, and 

H3N2. Limited accessions from a region can skew data and lead to misinterpretation and therefore, less 

inference can be applied to results from Regions 3, 4, and 5. 

National phylogenetic HA gene information 

HA genes from H1 subtype viruses are classified as alpha, beta, gamma, delta-1, delta-2, or pandemic 

H1N1 2009 (H1N1pdm09) phylogenetic clades based on a previously published nomenclature system. 

Similarly, H3 subtype viruses are classified as Cluster IV, Cluster IV-A, Cluster IV-B, Cluster IV-C, Cluster 

IV-D, Cluster IV-E, Cluster IV-F, or human-like. In the H1 subtypes (see Figure 9), there continued to be 

detections of alpha with two aa deletions (n=20). Delta 1a, delta 2, and gamma viruses are the 

predominant H1. 
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Figure 9. H1 phylo-cluster by region – 2-year summary Q2 FY 2016 to Q1 FY 2018

 
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Figure 10. H3 phylo-cluster by region, 2-year summary Q2 FY 2016 to Q1 FY 2018

In Q1 FY 2018, there were detections of human-like H3 in ten states and a new detection in AR. Out of 

65 H3s in Q1 FY 2018, 49 are human-like H3s. Human-like_2010 H3 is the predominant H3.

National phylogenetic NA gene information 

NA gene information remained the same in Q1 FY 2018. Both the N1 and N2 subtypes are found in 

circulating swine viruses. Classical N1 continued to be the dominant cluster. The 2002-lineage N2 

represents 84 percent of N2 collections. 
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Objective 2. Make influenza isolates from swine available for research and 

establish a data management system to facilitate genetic analysis of these 

isolates and related information

A primary goal of IAV-S surveillance is to share selected virus isolates obtained through the surveillance 

system with public health, animal health, and academic researchers to facilitate genetic analysis and 

research on viruses of interest. The NVSL Diagnostic Virology Laboratory maintains a repository of the 

viruses submitted into the surveillance system and provides these viruses upon request. 

In the first quarter of FY 2018, the NVSL Diagnostic Virology Laboratory provided 48 isolates to two

institutions: one governmental and one international (government). NVSL received 280 isolates into the 

repository in Q1 for a total of 280 in FY 2018 YTD (Table 4). Table 5 reports the total number of isolates 

available in the repository by subtype for sharing. 

 

Table 4. Virus isolates received in repository 

Virus isolates in the repository

2018 280

2017 844

2016 1,046

2015 883

2014 765

TOTAL TO DATE 3,818

Objective 3. Select proper isolates for development of relevant diagnostic 

reagents, updating diagnostic assays, and vaccine seed stock products

USDA makes IAV-S isolates available in the public domain for further research. ARS-NADC conducts 

research on isolates obtained from the repository and sequences generated from the surveillance 

system. Genetic sequencing reported to GenBank is available for private corporations, government 

entities, academia, and other scientific community partners for research and vaccine strain selection 

and efficacy testing. NVSL and ARS staff are consulted as subject matter experts when necessary. 

Table 5. Total number of subtyped 

isolates available through repository

Subtyped isolates available through 

repository

H3N2 1,469

H3N1 16

H1N1 1,913

H1N2 1,756

Mixed 298

TOTAL 5,452
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Conclusion

The IAV-S voluntary surveillance system continues to provide insight into the genetic makeup of 

circulating influenza virus in limited populations of commercial pigs. Genetic information and virus 

isolates are made publicly available for further research and possible vaccine strain selection and

efficacy testing. Influenza A virus in swine remains a dynamic virus with high levels of genetic variability 

in the hemagglutinin and neuraminidase genes. 
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Appendix 1. Regional Charts of HA and NA Combinations by Percentage

The following charts present the percentages of combinations of HA and NA on the national and 

regional scales based on ARS-NADC phylogenetic analyses. The results are reported from January 2016

to December 2017. These “heat maps” represent the percentage of combinations by using a color 

gradient; a deeper gradient represents a greater percentage occurrence for a particular HA-NA 

combination. HA clusters are listed on the left vertical axis of the chart and NA clusters are listed on the 

bottom horizontal axis. Line up the HA cluster with the corresponding NA cluster to determine the 

percentage of occurrence of that particular combination. 
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Total HA & NA combinations – 1,658
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Region 1. Total HA & NA combinations – 277
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Region 2. Total HA & NA combinations – 1,083
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Region 3. Total HA & NA combinations – 124
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Region 4. Total HA & NA combinations – 138
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Region 5. Total HA & NA combinations –7